GSVA_find_gs_markers: To find geneset markers of each cluster

In Lian-Lab/LIANLAB: To integrate analysis methods and simplify analysis process

Description

To find geneset markers of each cluster

Usage

GSVA_find_gs_markers(
  em = NULL,
  seurat_object = NULL,
  gspath = NULL,
  species = "mouse",
  adjPvalueCutoff = 0.001,
  filename = NULL,
  logFCcutoff = 0.1,
  text.size = 2,
  topn = 20,
  min.sz = 2,
  parallel.sz = 12
)

Arguments

em	expression matrix as genes in row, samples or cells in column
seurat_object	it also support a seurat_object instead of expression matrix
gspath	the correct path of your geneset file(.gmt)
species	species of the seurat.obj or matrix
adjPvalueCutoff	cutof the P.adjust
filename	the name of the generated file
logFCcutoff	cutof the logFC
text.size	the size of the text
topn	number of the top pathways
min.sz	minimum size of the resulting gene sets
parallel.sz	number of threads of execution to use when doing the calculations in parallel.

Value

seurat.obj with the marker_gs

Examples

## Not run: 
input.file <- system.file('extdata','pbmc_1k.RDS',package = 'LIANLABDATA')
pbmc_1k <- readRDS(input.file)
GSVA_pheatmap( seurat_object = pbmc_1k,species="mouse")

## End(Not run)

Lian-Lab/LIANLAB documentation built on June 23, 2021, 5:37 a.m.